11-31155713-T-A

Variant names:

• chr11-31155713-T-A
• rs400964
• NM_001387274.1:c.1222-17929A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001387274.1(DCDC1):​c.1222-17929A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 152,036 control chromosomes in the GnomAD database, including 25,202 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.57 (25202 hom., cov: 32)
• Consequence: DCDC1 NM_001387274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.646
• Publications: 4 publications found

Genes affected

DCDC1 (HGNC:20625): (doublecortin domain containing 1) This gene encodes a member of the doublecortin family. The protein encoded by this gene is a hydrophilic, intracellular protein. It contains a single doublecortin domain and is unable to bind microtubules and to regulate microtubule polymerization. This gene is mainly expressed in adult testis. It does not have a mouse homolog. [provided by RefSeq, Sep 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCDC1	NM_001387274.1	c.1222-17929A>T		intron_variant	Intron 9 of 38	ENST00000684477.1	NP_001374203.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCDC1	ENST00000684477.1	c.1222-17929A>T		intron_variant	Intron 9 of 38		NM_001387274.1	ENSP00000507427.1

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85922 AN: 151918 Hom.: 25196 Cov.: 32

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.555

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.565 AC: 85954 AN: 152036 Hom.: 25202 Cov.: 32 AF XY: 0.569 AC XY: 42255 AN XY: 74302

African (AFR) AF: 0.425 AC: 17605 AN: 41440

American (AMR) AF: 0.550 AC: 8397 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1852 AN: 3470

East Asian (EAS) AF: 0.930 AC: 4807 AN: 5170

South Asian (SAS) AF: 0.690 AC: 3327 AN: 4822

European-Finnish (FIN) AF: 0.596 AC: 6294 AN: 10558

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.616 AC: 41849 AN: 67984

Other (OTH) AF: 0.561 AC: 1182 AN: 2106

Alfa AF: 0.498 Hom.: 1585

Bravo AF: 0.552

Asia WGS AF: 0.797 AC: 2767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.7
DANN	Benign	0.81
PhyloP100		0.65
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs400964; hg19: chr11-31177260;